Traditional processes of drug discovery involve the screening of complex fermentation broths and plant extracts for a desired biological activity or the chemical synthesis of many new compounds for evaluation as potential drugs. The advantage of screening mixtures from biological sources is that a large number of compounds are screened simultaneously, in some cases leading to the discovery of novel and complex natural products with activity that could not have been predicted otherwise. The disadvantages are that many different samples must be screened and numerous purifications must be carried out to identify the active component, often present only in trace amounts. On the her hand, laboratory syntheses give unambiguous products, but the preparation of each new structure requires significant amounts of resources. Generally, the de novo design of active compounds based on the high resolution structures of enzymes has not been successful.
It is thus now widely appreciated that combinatorial libraries are useful per se and that such libraries and compounds comprising them have great commercial importance. Indeed, a branch of chemistry has developed to exploit the many commercial aspects of combinatorial libraries.
In order to maximize the advantages of each classical combinatorial approach, new strategies for combinatorial deconvolution have been developed independently by several groups. Selection techniques have been used with libraries of peptides (Geysen et al., J. Immun. Meth., 1987, 102, 259; Houghten et al., Nature, 1991, 354, 84; Owens et al., Biochem. Biophys. Res. Commun., 1991, 181, 402; Doyle, PCT WO 94/28424; Brennan, PCT WO 94/27719); nucleic acids (Wyatt et al., Proc. Natl. Acad. Sci. U.S.A., 1994, 91, 1356; Ecker et al., Nucleic Acids Res., 1993, 21, 1853); nonpeptides and small molecules (Simon et al., Proc. Natl. Acad. Sci. U.S.A., 1992, 89, 9367; Zuckermann et al., J. Am. Chem. Soc., 1992, 114, 10646; Bartlett et al., WO 91/19735; Ohlmeyer et al., Proc. Natl. Acad. Sci. U.S.A., 1993, 90, 10922; DeWitt et al., Proc. Natl. Acad. Sci. U.S.A., 1993, 90, 6909; Cody et al., U.S. Pat. No. 5,324,483; Houghten et al., PCT WO 94/26775; Ellman, U.S. Pat. No. 5,288,514; Still et al., WO 94/08051; Kauffman et al., PCT WO 94/24314; Carell et al., Angew. Chem. Int. Ed. Engl., 1994, 33, 2059; Carell et al., Angew. Chem. Int. Ed. Engel., 1994, 33, 2061; Lebl et al., WO 94/28028). A review of the above references reveals that the most advanced of these techniques are those for the selection of peptides and nucleic acids. Several groups are working on selection of heterocycles such as benzodiazepines.
The majority of the techniques reported to date involve iterative synthesis and screening of increasingly simplified subsets of oligomers such as peptides and oligonucleotides. Monomers or sub-monomers that have been utilized include amino acids, amino acid-like molecules, i.e. carbamate precursors, and nucleotides, both of which are bifunctional. Utilizing these techniques, libraries have been assayed for activity in either cell-based assays, or for binding and/or inhibition of purified protein targets.
However, the combinatorial chemical approach that has been more commonly utilized of late involves the use of a multifunctional scaffold bearing multiple diversity sites, and derivatizing these sites with varied building blocks to form libraries of diverse small molecule compounds. Libraries may be generated such that each individual compound may be synthesized and isolated separately, or synthesized and used as a mixture of several desirable compounds. A mixture of compounds may be obtained by using a mixture of scaffolds and/or building blocks. However, the synthesis of combinatorial libraries of discrete molecules (parallel synthesis) and of combinatorial pools of molecules (mixture synthesis or split-mix synthesis), and the screening of such libraries, have had significant limitations. These limitations include the need for selective protection and deprotection of desired reactive sites, limited experience with solid-phase chemical reactions, limited access to unique scaffolds for solid-phase synthesis, a small number of reactive functionalities on such scaffolds and often a small number of compound members of classes of building blocks that may be used for library generation. Acids, amines and amino acids are classes of building blocks that have been recognized to be of tremendous utility in combinatorial chemistry because of their reactivity with a variety of functional groups and the availability of large numbers of such compounds of diverse structures from commercial sources. Amino acids, for example, have been extensively used in the synthesis of small molecule combinatorial libraries. The use of amino acids as key building blocks in the construction of substituted heterocycle libraries has been practiced by several groups for exploring known pharmacophores, in cyclic ureas and in `prospecting libraries` (Bunin and Ellman, J. Am. Chem. Soc., 1992, 114, 10997; DeWitt et al., Proc. Natl. Acad. Sci. USA, 1993, 90, 6909; Nefzi, et al., Tetrahedron Lett., 1997, 38, 931; Bartlett, et al., Book of Abstracts, 213th American Chemical Society National Meeting, San Francisco, 1997, American Chemical Society, Washington D.C., ORGN-273).
The diversity of a combinatorial library is represented by the inherent physical and chemical properties of each scaffold and building block used, the number of different building blocks used during each derivatization step, the physical and chemical properties of the bonds arising from the derivatization chemistry, and the interactions of the scaffold and building block chemistries. Taken together, these interactions provide a unique conformation for each individual compound in the combinatorial library.
In spite of advances in the synthesis of libraries of compounds, there still remains a need in the art for molecules which have fixed preorganized geometry which matches that of target biomolecules, including proteins and enzymes, nucleic acids, and lipids. It is also apparent that when targeting intervention of ligand-receptor interactions of large biomolecular targets that often have large binding sites, active sites, or binding epitopes, the inhibitors, agonists and antagonists desired will also need to be appropriately large. Thus, molecules larger than conventional small molecule drugs, such as oligomeric peptidomimetics, peptoids, and nucleotides, are considered candidates for screening for such activity. Oligomeric molecules derived from other, and often novel preorganized or rigid scaffolds may also be of value when targeting such ligand-receptor interactions. Combinatorially derived libraries should contain compounds which are rigid, yet still possess sufficient flexibility. It is preferable that this be achieved via automated synthesis on solid supports. It is also desirable to have use of scaffolds of some rigidity with multiple sites of diversity that may be selectively reacted via appropriate deprotection schemes during combinatorial library generation. Further, such scaffolds should offer diversity sites that may be reacted with a variety of building blocks, especially those classes of building blocks that comprise a large number of member compounds, such as acids, amines and amino acids.